Jungfraujoch/writer/RugnuxResultBlocks.cpp

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include "RugnuxResultBlocks.h"

#include <sstream>

#include <gemmi/to_cif.hpp>     // write_cif_block_to_stream
#include <gemmi/to_mmcif.hpp>   // make_mmcif_block

PlacedModelMessage PlacedModelFromStructure(const gemmi::Structure &st, const UnitCell &cell,
                                            const std::string &data_space_group_name) {
    PlacedModelMessage p;
    p.name = st.name;
    p.unit_cell = cell;
    p.space_group_name = data_space_group_name;
    p.model_space_group_name = st.spacegroup_hm;
    bool has_aniso = false;
    for (const gemmi::Model &m : st.models)
        for (const gemmi::Chain &ch : m.chains)
            for (const gemmi::Residue &r : ch.residues)
                for (const gemmi::Atom &a : r.atoms) {
                    p.model_number.push_back(m.num);
                    p.chain.push_back(ch.name);
                    p.residue_name.push_back(r.name);
                    p.seq_num.push_back(*r.seqid.num);
                    p.icode.push_back(static_cast<uint8_t>(r.seqid.icode));
                    p.het_flag.push_back(static_cast<uint8_t>(r.het_flag));
                    p.subchain.push_back(r.subchain);
                    p.entity_id.push_back(r.entity_id);
                    p.label_seq.push_back(r.label_seq.value);
                    p.atom_name.push_back(a.name);
                    p.element.push_back(a.element.name());
                    p.altloc.push_back(static_cast<uint8_t>(a.altloc));
                    p.charge.push_back(a.charge);
                    p.x.push_back(a.pos.x);
                    p.y.push_back(a.pos.y);
                    p.z.push_back(a.pos.z);
                    p.b_iso.push_back(a.b_iso);
                    p.occupancy.push_back(a.occ);
                    p.aniso.insert(p.aniso.end(), {a.aniso.u11, a.aniso.u22, a.aniso.u33,
                                                   a.aniso.u12, a.aniso.u13, a.aniso.u23});
                    has_aniso = has_aniso || a.aniso.nonzero();
                }
    if (!has_aniso)
        p.aniso.clear();
    // Everything of the model but its coordinates (and what goes with them: cell, symmetry, scale), as the mmCIF
    // categories gemmi writes, for the writer to put back on _model.cif.
    gemmi::MmcifOutputGroups groups(true);
    groups.atoms = groups.cell = groups.symmetry = groups.scale = groups.atom_type = groups.origx = false;
    // _entry.id would otherwise be made up from the name, which the block carries anyway.
    groups.entry = st.info.count("_entry.id") > 0;
    std::ostringstream os;
    gemmi::cif::write_cif_block_to_stream(os, gemmi::make_mmcif_block(st, groups));
    p.metadata_mmcif = os.str();
    return p;
}